[Freesurfer] recon without normalization

Hello, When I run the function recon-all -subjid s00x -autorecon1 -autorecon2 -nonormalization I've got an ERROR message: Skull Stripping /root/trabajo/freesurfer/subjects/c1prueba/mri mri_watershed -T1 -brain_atlas /root/trabajo/freesurfer/average/RB_all_withskull_2008-03-26.gca

[Freesurfer] recon-all -all error with version 4.5

Dear all, I am encountering a problem with 'recon-all -all' with one subject using freesurfer version 4.5 which I did not encounter when using version 4.4. With the older version, the stream ran without error, whereas the processing produces the following error with version 4.5: ##

Re: [Freesurfer] recon-all -all error with version 4.5

did you run out of disk space? Is the file aseg.auto_noCCseg.label_intensities.txt writeable in the subject's dir? On Wed, 18 Nov 2009, Narly A Golestani wrote: > > > Dear all, > > I am encountering a problem with 'recon-all -all' with one subject using > freesurfer version 4.5 which I did not e

Re: [Freesurfer] recon-all -all error with version 4.5

Hi Bruce, There is plenty of disk space, and the 'aseg.auto_noCCseg.label_intensities.txt' file *has* successfully been written to the subject's 'mri' directory. best, Narly. On Wed, 18 Nov 2009, Bruce Fischl wrote: > did you run out of disk space? Is the file > aseg.auto_noCCseg.label_intensi

Re: [Freesurfer] recon-all -all error with version 4.5

if you run it again does it fail in the same place? If so, send us the subject and we'll take a look. Bruce On Wed, 18 Nov 2009, Narly A Golestani wrote: > > Hi Bruce, > > There is plenty of disk space, and the > 'aseg.auto_noCCseg.label_intensities.txt' file *has* successfully been > written to

Re: [Freesurfer] Best way to convert Philips par/rec to mgz

Dear Julie, The easiest way to preserve your data type would be to ask your Philips representative to switch DICOM export to 16 bit representation of the data. Alternatively, if you have access to an EasyVision console, you could try converting your .PAR/.REC into Analyze files with Philips' own

[Freesurfer] Average subject registration

Hi, I've made an average of my subjects using make_average_volume. I've registered each subject's orig.mgz with native-space diffusion images, and created a label-like binary image (1 for included voxels, 0 for everything else) which is in diffusion-space. I can register this back into the subjec

Re: [Freesurfer] White matter edits - when to do manual corrections?

1. No, if the surface is correct you are fine. 2. Not positive what you mean, but it looks fine to me. 3. The green is usually the "orig" surface, not the ?h.white one. This is also a non-cortical region, so I wouldn't worry about it cheers Bruce On Wed, 18 Nov 2009, Lena Palaniyappan wrote:

Re: [Freesurfer] recon-all -all error with version 4.5

I had got the same error output with v4.50 but not v4.01 for one of my subjects. I guessed that something might be wrong with the skull-strip process. So, I ran this step with different wsthresh values (from 20 to 30, increased by 1), and found that the brainmask looked very similar if the wsthresh

[Freesurfer] recon without normalization

Hello all, When I run the function recon-all -subjid s00x -autorecon1 -autorecon2 -nonormalization I've got an ERROR message: Skull Stripping /root/trabajo/freesurfer/subjects/c1prueba/mri mri_watershed -T1 -brain_atlas /root/trabajo/freesurfer/average/RB_all_withskull_2008-03-26.

Re: [Freesurfer] recon without normalization

Hi Africa, -nonormalization flag skips the step where T1.mgz is generated which is causing the error, as you mentioned. 001.mgz initiates the recon-all, but there are several other steps and files generated in the process. Please refer to this wiki to see which steps and the output at each st

[Freesurfer] research position in San Francisco, CA

Freesurfer users, We are looking for new and experienced brain imagers with a background in signal processing to work in our UCSF-affiliated research lab. Please apply at the following link if interested: http://jobs-ncire.icims.com/jobs/1448/job thank you, Brian _

[Freesurfer] registration to a template

Hi all, Does anyone have any recommendations for testing anatomical similarity between 2 different subjects? Jared ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon without normalization

Hi Africa, even if the script completed I doubt that it would generate reasonable results without intensity normalization. You are better off using the expert options to make it a gentler normalization (e.g. running mri_normalize with -b $n -g $g where n < 10 (the default) and g < 1. This wi

Re: [Freesurfer] recon-all -all error with version 4.5

Hi Xiangchuan, so you found recon-all stopped in the same place (writing aseg.auto_noCCseg.label_intensities.txt)? Bruce On Wed, 18 Nov 2009, Xiangchuan Chen wrote: > I had got the same error output with v4.50 but not v4.01 for one of my > subjects. I guessed that something might be wrong with